Texas Res-X and rhodamine Red-X, new derivatives of sulforhodamine 101 and lissamine rhodamine B with improved labeling and fluorescence properties

A novel nanoprobe for visually investigating the controversial role of miRNA-34a as an oncogene or tumor suppressor in cancer cells

MiRNA-targeted therapy has become a hot topic in current cancer research. The key to this treatment strategy is to clarify the specific role of miRNA in cancer. However, the roles of some miRNAs acting as oncogenic or tumor suppressors are still controversial, which are influenced by different tumor types, even in the same cancer type. Hence, we designed a novel fluorescent nanoprobe based on polydopamine nanoparticles (PDA NPs) for simultaneously detecting caspase-3 and miRNA-34a within living cells. The specific role of miRNA-34a in different cancer cells could be further identified by studying the expression alterations of caspase-3 and miRNA-34a. Confocal imaging indicated that miRNA-34a indeed acted as a tumor suppressor in anticancer drug-treated MCF-7 and HeLa cells, where the effect of miRNA-34a remains controversial. The designed nanoprobe can offer a promising approach to ascertain the oncogenic or tumor-suppressing role of miRNA in different cancer cells with a simple visualization method, which has valuable implications for exploring the practicability of precision therapy focused on miRNA and evaluating the efficacy of new miRNA-targeted anticancer medications.

N-Functionalized fluorophores: detecting urinary albumin and imaging lipid droplets

A series of novel N-sulfonyl pyridinium fluorophores were designed, synthesized, and explored in terms of their ability to bind with serum albumins. Upon binding the fluorophores with BSA, noticeable emission wavelength or intensity changes accompanied by color changes were observed. Competitive binding studies revealed that the fluorophore selectively binds to the warfarin site, but the binding affinity also depends on the nature of the scaffold. Additionally, the fluorophores were employed to detect spiked serum albumin in artificial urine. Cellular imaging experiments indicated that the fluorophores accumulate within lipid droplets (LDs), suggesting their potential as promising biomarkers for lipid droplets. Furthermore, the fluorescence intensity, number, and size of LDs increased upon serum starvation.

Red-Shift (2-Hydroxyphenyl)-Benzothiazole Emission by Mimicking the Excited-State Intramolecular Proton Transfer Effect

Novel strategies to optimize the photophysical properties of organic fluorophores are of great significance to the design of imaging probes to interrogate biology. While the 2-(2-hydroxyphenyl)-benzothiazole (HBT) fluorophore has attracted considerable attention in the field of fluorescence imaging, its short emission in the blue region and low quantum yield restrict its wide application. Herein, by mimicking the excited-state intramolecular proton transfer (ESIPT) effect, we designed a series of 2-(2-hydroxyphenyl)-benzothiazole (HBT) derivatives by complexing the heteroatoms therein with a boron atom to enhance the chance of the tautomerized keto-like resonance form. This strategy significantly red-shifted the emission wavelengths of HBT, greatly enhanced its quantum yields, and caused little effect on molecular size. Typically, compounds 12B and 13B were observed to emit in the near-infrared region, making them among the smallest organic structures with emission above 650 nm.

Quantitative Imaging of Biochemistry in Situ and at the Nanoscale

Biochemical reactions in eukaryotic cells occur in subcellular, membrane-bound compartments called organelles. Each kind of organelle is characterized by a unique lumenal chemical composition whose stringent regulation is vital to proper organelle function. Disruption of the lumenal ionic content of organelles is inextricably linked to disease. Despite their vital roles in cellular homeostasis, there are large gaps in our knowledge of organellar chemical composition largely from a lack of suitable probes. In this Outlook, we describe how, using organelle-targeted ratiometric probes, one can quantitatively image the lumenal chemical composition and biochemical activity inside organelles. We discuss how excellent fluorescent detection chemistries applied largely to the cytosol may be expanded to study organelles by chemical imaging at subcellular resolution in live cells. DNA-based reporters are a new and versatile platform to enable such approaches because the resultant probes have precise ratiometry and accurate subcellular targeting and are able to map multiple chemicals simultaneously. Quantitatively mapping lumenal ions and biochemical activity can drive the discovery of new biology and biomedical applications.

Multiple-Labeled Antibodies Behave Like Single Emitters in Photoswitching Buffer

The degree of labeling (DOL) of antibodies has so far been optimized for high brightness and specific and efficient binding. The influence of the DOL on the blinking performance of antibodies used in direct stochastic optical reconstruction microscopy (dSTORM) has so far attained limited attention. Here, we investigated the spectroscopic characteristics of IgG antibodies labeled at DOLs of 1.1-8.3 with Alexa Fluor 647 (Al647) at the ensemble and single-molecule level. Multiple-Al647-labeled antibodies showed weak and strong quenching interactions in aqueous buffer but could all be used for dSTORM imaging with spatial resolutions of ∼20 nm independent of the DOL. Single-molecule fluorescence trajectories and photon antibunching experiments revealed that individual multiple-Al647-labeled antibodies show complex photophysics in aqueous buffer but behave as single emitters in photoswitching buffer independent of the DOL. We developed a model that explains the observed blinking of multiple-labeled antibodies and can be used for the development of improved fluorescent probes for dSTORM experiments.

The Spectrophotometric Characteristic of Immunoglobulin Conjugates for Diagnostics of Causative Agents of Especially Dangerous Infections

The possibility of characterizing fluorescent immunoglobulins using spectrophotometric analysis as a testing method is considered. The comparative analysis of optical properties of fluorescent immunoglobulin preparations and their components-immunoglobulins and fluorochrome-is carried out. The obtained results testify that the proposed methodological approach of optical detection of labeled immunoglobulin molecules can be promising for tests on obtaining conjugates used in immunological tests on revealing specific antigens of causative agents of especially dangerous infections.

Synthesis of [18F]2B-SRF101: A Sulfonamide Derivative of the Fluorescent Dye Sulforhodamine 101

BACKGROUND

The red fluorescent dye Sulforhodamine 101 (SR101) has been used in neuroscience research as a useful tool for staining of astrocytes, since it has been reported as a marker of astroglia in the neocortex of rodents in vivo. The aim of this work is to label SR101 with positron emission radionuclides, in order to provide a radiotracer to study its biological behavior. This is the first attempt to label SR101 by [18F], using a chemical derivatization via a sulfonamidelinker and a commercially available platform.

METHODS

The synthesis of SR101 N-(3-Bromopropyl) sulfonamide and SR101 N-(3- Fluoropropyl) sulfonamide (2B-SRF101) was carried out. The radiosynthesis of SR101 N-(3- [18F]Fluoropropyl) sulfonamide ([18F]2B-SRF101) was performed in a TRACERlab® FX-FN. Different labeling conditions were tested. Three pilot batches were produced and quality control was performed. Lipophilicity, plasma protein binding and radiochemical stability of [18F]2BSRF101 in final formulation and in plasma were determined.

RESULTS

SR101 N-(3-Bromopropyl) sulfonamide was synthetized as a precursor for radiolabeling with [18F]. 2B-SRF101 was prepared for analytical purpose. [18F]2B-SRF101 was obtained with radiochemical purity of (97.0 ± 0.6%). The yield of the whole synthesis was (11.9 ± 1.7 %), nondecay corrected. [18F]2B-SRF101 was found to be stable in final formulation and in plasma. The octanol-water partition coefficient was (Log POCT = 1.88 ± 0.14). The product showed a high percentage of plasma protein binding.

CONCLUSIONS

The derivatization of SR101 via sulfonamide-linker and the first radiosynthesis of [18 F]2B-SRF101 were performed. It was obtained in accordance with quality control specifications. In vitro stability studies verified that [18F]2B-SRF101 was suitable for preclinical evaluations.

Ophthalmic Combination of SurR9-C84A and Trichostatin-A Targeting Molecular Pathogenesis of Alkali Burn

Background: Alkali burn is a frequently occurring ocular injury that resembles ocular inflammation caused by eye allergies, infection, and refractive surgeries.

Methods: We investigated the synergistic regenerative potential of dominant negative survivin mutant (SurR9-C84A) and histone deacetylase (HDAC) inhibitor trichostatin-A (TSA) against alkali burn and corneal haze using human keratocytes and rabbit alkali burn model (Female New Zealand white rabbits).

Results: Combination of SurR9-C84A and TSA suppressed levels of transforming growth factor (TGF)-β, alpha smooth-muscle actin (α-SMA), fibronectin and HDAC1, leading to apoptosis in myofibroblast cells and, showed the potential to clear the corneal haze. An insult with 0.5 N NaOH for 1 min led to neutrophils infiltration and formation of large vacuoles in the stroma. Treatments with TSA and SurR9-C84A for 40 min led to improvement in the conjunctival and corneal tissue integrity, marked by an increase in clathrin, and claudin expressions. An increase in TGF-β and endogenous survivin confirmed wound healing and cell proliferation in rabbit cornea. The blood analysis revealed a substantial decrease in the RBC, WBC, platelets, or the hemoglobin content post alkali burn. The cytokine array analysis revealed that NaOH induced expressions of IL-1α and MMP-9, which were found to be significantly downregulated (1.8 and 11.5 fold respectively) by the combinatorial treatment of SurR9-C84A and TSA.

Conclusion: Our results confirmed that combination of SurR9-C84A with TSA worked in synergy to heal ocular injury and inflammations due to alkali burn and led to the regeneration of ocular tissue by increasing clathrin, claudin, survivin, and TGF-β and reversal of alkali burn by suppressing IL-1α and MMP-9 without inducing haze.

Semi-automated rapid quantification of brain vessel density utilizing fluorescent microscopy

BACKGROUND

Measurement of vascular density has significant value in characterizing healthy and diseased tissue, particularly in brain where vascular density varies among regions. Further, an understanding of brain vessel size helps distinguish between capillaries and larger vessels like arterioles and venules. Unfortunately, few cutting edge methodologies are available to laboratories to rapidly quantify vessel density.

NEW METHOD

We developed a rapid microscopic method, which quantifies the numbers and diameters of blood vessels in brain. Utilizing this method we characterized vascular density of five brain regions in both mice and rats, in two tumor models, using three tracers.

RESULTS

We observed the number of sections/mm(2) in various brain regions: genu of corpus callosum 161±7, hippocampus 266±18, superior colliculus 300±24, frontal cortex 391±55, and inferior colliculus 692±18 (n=5 animals). Regional brain data were not significantly different between species (p>0.05) or when using different tracers (70kDa and 2000kDa Texas Red; p>0.05). Vascular density decreased (62-79%) in preclinical brain metastases but increased (62%) a rat glioma model.

COMPARISON WITH EXISTING METHODS

Our values were similar (p>0.05) to published literature. We applied this method to brain-tumors and observed brain metastases of breast cancer to have a ∼2.5-fold reduction (p>0.05) in vessels/mm(2) compared to normal cortical regions. In contrast, vascular density in a glioma model was significantly higher (sections/mm(2) 736±84; p<0.05).

CONCLUSIONS

In summary, we present a vascular density counting method that is rapid, sensitive, and uses fluorescence microscopy without antibodies.

Fluorescent Bisphosphonate and Carboxyphosphonate Probes: A Versatile Imaging Toolkit for Applications in Bone Biology and Biomedicine

A bone imaging toolkit of 21 fluorescent probes with variable spectroscopic properties, bone mineral binding affinities, and antiprenylation activities has been created, including a novel linking strategy. The linking chemistry allows attachment of a diverse selection of dyes fluorescent in the visible to near-infrared range to any of the three clinically important heterocyclic bisphosphonate bone drugs (risedronate, zoledronate, and minodronate or their analogues). The resultant suite of conjugates offers multiple options to "mix and match" parent drug structure, fluorescence emission wavelength, relative bone affinity, and presence or absence of antiprenylation activity, for bone-related imaging applications.

Bright Fluorescent Nanotags from Bottlebrush Polymers with DNA-Tipped Bristles

Bright signal outputs are needed for fluorescence detection of biomolecules at their native expression levels. Increasing the number of labels on a probe often results in crowding-induced self-quenching of chromophores, and maintaining the function of the targeting moiety (e.g., an antibody) is a concern. Here we demonstrate a simple method to accommodate thousands of fluorescent dye molecules on a single antibody probe while avoiding the negative effects of self-quenching. We use a bottlebrush polymer from which extend hundreds of duplex DNA strands that can accommodate hundreds of covalently attached and/or thousands of noncovalently intercalated fluorescent dyes. This polymer-DNA assembly sequesters the intercalated fluorophores against dissociation and can be tethered through DNA hybridization to an IgG antibody. The resulting fluorescent nanotag can detect protein targets in flow cytometry, confocal fluorescence microscopy, and dot blots with an exceptionally bright signal that compares favorably to commercially available antibodies labeled with organic dyes or quantum dots.

Interaction of Lysinibacillus sphaericus binary toxin with mosquito larval gut cells: Binding and internalization

The binary toxin produced by Lysinibacillus sphaericus is composed of BinA and BinB subunits. Together, but not separately, the two subunits are highly toxic to Culex quinquefasciatus larvae, but show no toxicity to Aedes aegypti. The molecular mechanism underlying intoxication has not been clearly elucidated. The present study compares the binding and the internalization of binary toxin into the midgut epithelial cells of susceptible C. quinquefasciatus mosquito larvae with those of Bin-refractory A. aegypti. The guts from larvae fed with fluorescently labeled toxin were dissected and analyzed using a confocal laser scanning microscope. When fed with a mixture of both components, co-localization of BinA and BinB was detected both on the cell surface and in the cytoplasm of Culex larval gut cells. However, administration of BinA alone resulted in localization only on the cell membrane, whereas BinB alone was detected both on the cell membrane and inside the cytoplasm. In contrast, when a mixture of both components, or each individual component, was fed to Aedes larvae, BinA and BinB were unable to reach the cytoplasm and were localized only on the cell membrane. These results are consistent with the suggestion that the internalization of BinA is essential for toxicity, and that BinB is required for this internalization into susceptible larval gut cells.

Developments and recent advancements in the field of endogenous amino acid selective bond forming reactions for bioconjugation

Bioconjugation methodologies have proven to play a central enabling role in the recent development of biotherapeutics and chemical biology approaches. Recent endeavours in these fields shed light on unprecedented chemical challenges to attain bioselectivity, biocompatibility, and biostability required by modern applications. In this review the current developments in various techniques of selective bond forming reactions of proteins and peptides were highlighted. The utility of each endogenous amino acid-selective conjugation methodology in the fields of biology and protein science has been surveyed with emphasis on the most relevant among reported transformations; selectivity and practical use have been discussed.

The zebrafish merovingian mutant reveals a role for pH regulation in hair cell toxicity and function

Control of the extracellular environment of inner ear hair cells by ionic transporters is crucial for hair cell function. In addition to inner ear hair cells, aquatic vertebrates have hair cells on the surface of their body in the lateral line system. The ionic environment of these cells also appears to be regulated, although the mechanisms of this regulation are less understood than those of the mammalian inner ear. We identified the merovingian mutant through genetic screening in zebrafish for genes involved in drug-induced hair cell death. Mutants show complete resistance to neomycin-induced hair cell death and partial resistance to cisplatin-induced hair cell death. This resistance is probably due to impaired drug uptake as a result of reduced mechanotransduction ability, suggesting that the mutants have defects in hair cell function independent of drug treatment. Through genetic mapping we found that merovingian mutants contain a mutation in the transcription factor gcm2. This gene is important for the production of ionocytes, which are cells crucial for whole body pH regulation in fish. We found that merovingian mutants showed an acidified extracellular environment in the vicinity of both inner ear and lateral line hair cells. We believe that this acidified extracellular environment is responsible for the defects seen in hair cells of merovingian mutants, and that these mutants would serve as a valuable model for further study of the role of pH in hair cell function.

Red-shifted fluorescent aminated derivatives of a conformationally locked GFP chromophore

A novel class of fluorescent dyes based on conformationally locked GFP chromophore is reported. These dyes are characterized by red-shifted spectra, high fluorescence quantum yields and pH-independence in physiological pH range. The intra- and intermolecular mechanisms of radiationless deactivation of ABDI-BF2 fluorophore by selective structural locking of various conformational degrees of freedom were studied. A unique combination of solvatochromic and lipophilic properties together with "infinite" photostability (due to a dynamic exchange between free and bound dye) makes some of the novel dyes promising bioinspired tools for labeling cellular membranes, lipid drops and other organelles.

Lanthanide(III) complexes of rhodamine-DO3A conjugates as agents for dual-modal imaging

Two novel dual-modal MRI/optical probes based on a rhodamine-DO3A conjugate have been prepared. The bis(aqua)gadolinium(III) complex Gd.L1 and mono(aqua)gadolinium(III) complex Gd.L2 behave as dual-modal imaging probes (r1 = 8.5 and 3.8 mM(-1) s(-1) for Gd.L1 and Gd.L2, respectively; λex = 560 nm and λem = 580 nm for both complexes). The rhodamine fragment is pH-sensitive, and upon lowering of the pH, an increase in fluorescence intensity is observed as the spirolactam ring opens to give the highly fluorescent form of the molecule. The ligands are bimodal when coordinated to Tb(III) ions, inducing fluorescence from both the lanthanide center and the rhodamine fluorophore, on two independent time frames. Confocal imaging experiments were carried out to establish the localization of Gd.L2 in HEK293 cells and primary mouse islet cells (∼70% insulin-containing β cells). Colocalization with MitoTracker Green demonstrated Gd.L2's ability to distinguish between tumor and healthy cells, with compartmentalization believed to be in the mitochondria. Gd.L2 was also evaluated as an MRI probe for imaging of tumors in BALB/c nude mice bearing M21 xenografts. A 36.5% decrease in T1 within the tumor was observed 30 min post injection, showing that Gd.L2 is preferentially up taken in the tumor. Gd.L2 is the first small-molecule MR/fluorescent dual-modal imaging agent to display an off-on pH switch upon its preferential uptake within the more acidic microenvironment of tumor cells.

Optical imaging of tumors with copper-labeled rhodamine derivatives by targeting mitochondria

In this study, we evaluated Cu(L1) in two xenografted tumor-bearing (U87MG and MDA-MB-435) animal models to prove the concept that Cu(II)-labeled rhodamine derivatives, Cu(L) (L = L1 - L4) are useful as selective fluorescent probes for tumor imaging. We found that both multidrug resistance (MDR) negative U87MG gliomas and MDR-positive MDA-MB-435 breast tumors could be visualized. Because of tissue attenuation, accurate quantification of tumor uptake was difficult by optical methods. Therefore, ⁶⁴Cu(L) (L = L1 - L4) were evaluated to compare their biodistribution properties. It was found that all four ⁶⁴Cu radiotracers had a high glioma uptake (⁶⁴Cu(L1): 5.71± 1.43 %ID/g; ⁶⁴Cu(L2): 5.98 ± 2.75 %ID/g; ⁶⁴Cu(L3): 4.28 ± 1.45 %ID/g; and ⁶⁴Cu(L4): 6.25 ± 3.42 %ID/g) with ⁶⁴Cu(L1) showing the highest tumor/background ratios. In athymic nude mice bearing MDA-MB-435 breast cancer xenografts, ⁶⁴Cu(L4) showed almost identical normal organ uptake to that in the glioma-bearing animals, but its breast tumor uptake (1.26 ± 0.10% ID/g) was significantly lower (p < 0.001) than that in the glioma (6.25 ± 3.42% ID/g) because of MDR Pgps (P-glycoproteins) and MRPs (multidrug resistance-associated proteins) overexpressed in the xenografted MDA-MB-435 breast tumors. Results from cellular staining assays showed that both Cu(L2) and Cu(L4) were able to localize in mitochondria of U87MG cells, and their tumor selectivity was caused by the elevated negative mitochondrial potential in U87MG glioma cells as compared to that in human fibroblast cells. On the basis of these results, it was concluded that Cu(L) (L = L1 - L4) are useful as selective fluorescent probes for cellular staining assays and optical tumor imaging while ⁶⁴Cu(L) (L = L1 - L4) have the potential as PET radiotracers for tumor imaging. This study represents a good example of dual modality imaging (PET and optical) using two agents, ⁶⁴Cu(L) and Cu(L), with identical chemical composition. Future research will focus on developing new fluorescent probes with longer wavelength and reduced liver uptake.

Time-gated luminescence microscopy with responsive nonmetal probes for mapping activity of protein kinases in living cells

A photoluminescence probe ARC-1185, possessing both high affinity towards basophilic protein kinases (PKs) and microsecond-scale luminescence lifetime when associated with a kinase, was used for the mapping of ARC-1185-PK complexes in living cells with time-gated luminescence microscopy.

64Cu-labeled phosphonium cations as PET radiotracers for tumor imaging

Alteration in mitochondrial transmembrane potential (ΔΨ(m)) is an important characteristic of cancer. The observation that the enhanced negative mitochondrial potential is prevalent in tumor cell phenotype provides a conceptual basis for development of mitochondrion-targeting therapeutic drugs and molecular imaging probes. Since plasma and mitochondrial potentials are negative, many delocalized organic cations, such as rhodamine-123 and (3)H-tetraphenylphosphonium, are electrophoretically driven through these membranes, and able to localize in the energized mitochondria of tumor cells. Cationic radiotracers, such as (99m)Tc-Sestamibi and (99m)Tc-Tetrofosmin, have been clinically used for diagnosis of cancer by single photon emission computed tomography (SPECT) and noninvasive monitoring of the multidrug resistance (MDR) transport function in tumors of different origin. However, their diagnostic and prognostic values are often limited due to their insufficient tumor localization (low radiotracer tumor uptake) and high radioactivity accumulation in the chest and abdominal regions (low tumor selectivity). In contrast, the (64)Cu-labeled phosphonium cations represent a new class of PET (positron emission tomography) radiotracers with good tumor uptake and high tumor selectivity. This review article will focus on our recent experiences in evaluation of (64)Cu-labeled phosphonium cations as potential PET radiotracers. The main objective is to illustrate the impact of radiometal chelate on physical, chemical, and biological properties of (64)Cu radiotracers. It will also discuss some important issues related to their tumor selectivity and possible tumor localization mechanism.

NEAR-INFRARED DYES: Probe Development and Applications in Optical Molecular Imaging

The recent emergence of optical imaging has brought forth a unique challenge for chemists: development of new biocompatible dyes that fluoresce in the near-infrared (NIR) region for optimal use in biomedical applications. This review describes the synthesis of NIR dyes and the design of probes capable of noninvasively imaging molecular events in small animal models.

64Cu-labeled lissamine rhodamine B: a promising PET radiotracer targeting tumor mitochondria

Enhanced mitochondrial potential in carcinoma cells is an important characteristic of cancer. It is of great current interest to develop a radiotracer that is sensitive to mitochondrial potential changes at the early stage of tumor growth. In this report, we present the synthesis and evaluation of (64)Cu-labeled Lissamine rhodamine B (LRB), (64)Cu(DOTA-LRB) (DOTA-LRB = 2-(6-(diethylamino)-3-(diethyliminio)-3H-xanthen-9-yl)-5-(N-(2-(2-(4,7,10-tris(carboxymethyl)-1,4,7,10-tetraazacyclo-dodecan-1-yl)acetamido)ethyl)sulfamoyl)benzenesulfonate) as a new radiotracer for imaging tumors in athymic nude mice bearing U87MG human glioma xenografts by positron emission tomography (PET). We also explored its localization mechanism using Cu(DOTA-LRB) as the fluorescent probe in both the U87MG human glioma cell line and the cultured primary U87MG glioma cells. It was found that (64)Cu(DOTA-LRB) had the highest tumor uptake (6.54 ± 1.50, 6.91 ± 1.26, 5.68 ± 1.13, 7.58 ± 1.96, and 5.14 ± 1.50%ID/g at 0.5, 1, 2, 4, and 24 h postinjection, respectively) among many (64)Cu-labeled organic cations evaluated in the same animal model. The cellular staining study indicated that Cu(DOTA-LRB) was able to localize in mitochondria of U87MG glioma cells due to the enhanced negative mitochondrial potential. This statement is completely supported by the results from decoupling experiment with carbonylcyanide-m-chlorophenylhydrazone (CCCP). MicroPET data showed that the U87MG glioma tumors were clearly visualized as early as 30 min postinjection with (64)Cu(DOTA-LRB). (64)Cu(DOTA-LRB) remained stable during renal excretion, but underwent extensive degradation during hepatobiliary excretion. On the basis of the results from this study, it was concluded that (64)Cu(DOTA-LRB) represents a new class of promising PET radiotracers for noninvasive imaging of the MDR-negative tumors.

A new class of cleavable fluorescent nucleotides: synthesis and optimization as reversible terminators for DNA sequencing by synthesis

Fluorescent 2′-deoxynucleotides containing a protecting group at the 3′-O-position are reversible terminators enabling array-based DNA sequencing by synthesis (SBS) approaches. Herein, we describe the synthesis of a new family of 3′-OH unprotected cleavable fluorescent 2′-deoxynucleotides and their evaluation as reversible terminators for high-throughput DNA SBS strategies. In this first version, all four modified nucleotides bearing a cleavable disulfide Alexa Fluor® 594 dye were assayed for their ability to act as a reversible stop for the incorporation of the next labeled base. Their use in SBS leaded to a signal–no signal output after successive addition of each labeled nucleotide during the sequencing process (binary read-out). Solid-phase immobilized synthetic DNA target sequences were used to optimize the method that has been applied to DNA polymerized colonies or clusters obtained by in situ solid-phase amplification of fragments of genomic DNA templates.

Selective uptake of surface-modified phospholipid vesicles by bone marrow macrophages in vivo

An advantage of using vesicles (liposomes) as drug delivery carriers is that their pharmacokinetics can be controlled by surface characteristics, which can permit specific delivery of the encapsulated agents to organs or cells in vivo. Here we report a vesicle formulation which targets the bone marrow after intravenous injection in rabbits. Surface modification of the vesicle with an anionic amphiphile; L-glutamic acid, N-(3-carboxy-1-oxopropyl)-, 1,5-dihexadecyl ester (SA) results in significant targeting of vesicles to bone marrow. Further incorporation of as little as 0.6 mol% of poly(ethylene glycol)-lipid (PEG-DSPE) passively enhanced the distribution of SA-vesicles into bone marrow and inhibited hepatic uptake. In this model, more than 60% of the intravenously injected vesicles were distributed to bone marrow within 6 h after administration of a small dose of lipid (15 mg/kg b.w.). Histological evidence indicates that the targeting was achieved due to uptake by bone marrow macrophages (BMMphi). The efficient delivery of encapsulated scintigraphic and fluorescent imaging agents to BMMphi suggests that vesicles are promising carriers for the specific targeting of BMMphi and may be useful for delivering a wide range of therapeutic agents to bone marrow.

Enhancement of Adsorbed Dye Monolayer Fluorescence by a Silver Nanoparticle Overlayer

Deposition of silver nanoparticles directly onto a Rhodamine Red monolayer covalently bound to glass is found to increase the photoluminescence by as much as 20 times depending on excitation wavelength and nanoparticle density. At the same time, the excited state lifetime is reduced by more than a factor of 2, the fluorescence spectrum is blue-shifted, and greater polarization anisotropy in the emission is observed. We attribute these effects to local enhancement of the optical fields near the molecules by interactions with silver plasmons. We approximately separate the relative contributions of increased absorption and increased emissive rate to the observed enhancement of fluorescence. A study of the spatial inhomogeneity of the effect using scanning confocal microscopy demonstrates that average enhancements at least twice as large are possible.

BTA, a novel reagent for DNA attachment on glass and efficient generation of solid-phase amplified DNA colonies

The tricarboxylate reagent benzene-1,3,5-triacetic acid (BTA) was used to attach 5′-aminated DNA primers and templates on an aminosilanized glass surface for subsequent generation of DNA colonies by in situ solid-phase amplification. We have characterized the derivatized surfaces for the chemical attachment of oligonucleotides and evaluate the properties relevant for the amplification process: surface density, thermal stability towards thermocycling, functionalization reproducibility and storage stability. The derivatization process, first developed for glass slides, was then adapted to microfabricated glass channels containing integrated fluidic connections. This implementation resulted in an important reduction of reaction times, consumption of reagents and process automation. Innovative analytical methods for the characterization of attached DNA were developed for assessing the surface immobilized DNA content after amplification. The results obtained showed that the BTA chemistry is compatible and suitable for forming highly dense arrays of DNA colonies with optimal surface coverage of about 10 million colonies/cm² from the amplification of initial single-template DNA molecules immobilized. We also demonstrate that the dsDNA colonies generated can be quantitatively processed in situ by restriction enzymes digestion. DNA colonies generated using the BTA reagent can be used for further sequence analysis in an unprecedented parallel fashion for low-cost genomic studies.

Integrated microsystem for dielectrophoretic cell concentration and genetic detection

We have directly integrated a continuous-flow, electrokinetic method of bacterial cell concentration with room temperature, sequence-specific genetic detection. The system we have developed traps cells from a continuous-flow sample stream via dielectrophoresis, providing a 160-fold increase in cell concentration. PDMS microvalves then define a 100 nL volume around the trapped cells to which cell lysis buffer and genetic detection components are introduced. Direct, optical detection of Escherichia coli MC1061 cells is then accomplished via the sequence-specific hybridization of an rRNA-directed optical molecular beacon. This integrated microsystem is capable of sequence-specific genetic detection of 25 cells within 30 min.

Hydrophilic labeling reagents of dipyrrylmethene-BF2 dyes for two-photon excited fluorometry: syntheses and photophysical characterization

Recently introduced bioaffinity assay technology, ArcDia TPX, is based on two-photon excited fluorescence (TPE) and it enables separation-free ultra-sensitive immunoassays from microvolumes. Here we present syntheses of novel two-photon excitable fluorescent labeling reagents which have been specially designed to be used as label molecules in the ArcDia TPX assay technique. The labeling reagents are based on dipyrrylmetheneboron difluoride (dipyrrylmethene-BF2) chromophore, which have been substituted with aryl, heteroaryl or arylalkenyl chemical groups to extend the pi-electron conjugation. These substitutions results in a series of dipyrrylmethene-BF2 fluorophores with different photophysical properties. Dipyrrylmethene-BF2 fluorophores have been further substituted with a dipeptide linker unit and finally activated as succinimidyl esters to enable specific coupling with primary amino groups. The dipeptide linker serves as a spacer arm between the label and a target, and enhances the solubility of the label in aqueous solutions. Study of the chemical and photophysical performance of the new labeling reagents is described. The new labeling reagents exhibit high fluorescence quantum yields, and molar absorption coefficients. The results show that the new labels with the hydrophilic dipeptide linker unit provide large two-photon excitation cross-sections, high fluorescence quantum efficiency and good solubility in aqueous solutions. The results suggest that the novel dipyrrylmethene-BF2 labels are highly applicable to bioaffinity assays based on two-photon excitation of fluorescence.

High-throughput fluorescence spectroscopic analysis of affinity of peptides displayed on bacteriophage

Fluorescence spectroscopy titrations, although widely used to analyze binding affinity, are not an efficient screening method for detecting high-affinity binding among a large number of available ligands, such as during bacteriophage display selections. We hypothesize that a miniaturized, high-throughput fluorescence spectroscopy assay can be used to efficiently analyze selection results by applying the Langmuir equation to the binding data to estimate affinity constants for a large number of ligands, either as synthesized molecules or as displayed on bacteriophage. Here, bacteriophage-display-derived peptides specific for the Thomsen-Friedenreich disaccharide are used to develop a high-throughput fluorescence spectroscopy screening method, which uses one binding partner labeled with a fluorescent dye and different concentrations of a second partner to analyze binding affinity in bacteriophage display selections. The affinity constants derived from binding isotherms prepared using the new system accurately replicate those derived from standard spectroscopy titrations. Furthermore, the technique correctly defined the affinity constant describing binding of a cognate epitope peptide by a monoclonal antibody. Finally, we have applied the technique to analysis of binding affinity by ligands displayed on bacteriophage, which suggests that this technique could be used to monitor bacteriophage enrichment during selections.